X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=3538ff4b1738f95e0516332b803c139306ed7206;hb=d82d17a7ba88f90e6b8b1b591245a7ee70b3975c;hp=f8de1f0b610ee1076612e8109a404c5c3ee97c15;hpb=21c2deb35c435e6097b0f05c83d21cfdf4929ba2;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index f8de1f0..3538ff4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,61 +24,48 @@

- What's new in Jalview 2.10 ? + Jalview 2.11 - major and minor new features +

Jalview 2.11 introduces support for loading VCF files, and new + filters and shading models for sequence features. Under the hood, + we've addressed many bugs, and also made some important changes in + the way the Jalview desktop is installed and launched.

VCF Support. Proteins and genomic contigs with + chromosomal location annotation (such as protein coding genes + retrieved from Ensembl) can be annotated with variants imported + from a local VCF file.
The Jalview Launcher and Update System
+ Jalview's new installation model means you'll only need to + download and install Jalview once. After installation, Jalview + will automatically keep itself up to date. The launcher also sets + Jalview's memory automatically, so you'll never again have to + manually configure Java's memory settings.
We are grateful to + Install4J who provided us with a free license for their + installation system, and Jalview's over the air update system is + via Getdown.

+ The full list of bugs fixed in this release can be found in the 2.11 Release Notes.

- Jalview 2.10 is the next major release in the Jalview 2 series. Full - details are in the Jalview - 2.10 Release Notes, but the highlights are below. + Jalview and Java 11, 13, and onwards

Java 11 provides improved performance and better OS + integration, so we now recommend users select our Java 11 Jalview + distribution rather than the legacy Java 8 build.

+ Known Issues - update for 211

Ensembl sequence fetcher. Annotated Genes, - transcripts and proteinsÂ can be retrieved via Jalview's new Ensembl REST - client. Support for import of Ensembl data allows: -
- Sequence variant data. Jalview - propagates variant annotation on genomic regions onto - transcripts and protein products, complete with associated - metadata such as clinical significance.
- Aligned locus view. Transcripts - retrieved for a gene identifier via the Ensembl or - EnsemblGenomes sequence databases are automatically aligned to - their reference genome, and introns hidden from the view.
Working with structures. -
- More accurate structure mappings. - Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) - to match structures - to UniProt sequences, even for structures containing - multiple copies of a sequence.
- Import structures as mmCIF. Jalview - now downloads data from the EMBL-EBI's PDBe site as mmCIF. This allows very large - structures to be imported, such as the HIV virus capsid - assembly.
- Chimera users will need to upgrade to - 1.11.1.If you use Chimera to view structures downloaded by - Jalview 2.10, you will need to make sure you are running the - latest version of Chimera.
UniProt Free Text Search. The new search - dialog for UniProt allows you to browse and retrieve sequences - from UniProt with free-text search and more structured queries
Reference sequence alignment view.. - Jalview 2.9 introduced support for reference sequences. In 2.10, - when a reference sequence is defined for the alignment, the - alignment column ruler is now numbered according to the reference - sequence. The reference sequence for alignment views can also be - saved and restored from Jalview projects.
Ensembl and ENA 'show cross-references' - support.The Calculations menu's 'Show - cross-references' will now offer Ensembl as well as EMBLCDS and - Uniprot when CDS/Protein mapping data is available for download or - display.
OSX: The 'Open File' dialog for Jalview's Groovy Console + appears with the title 'Save As', and attempting to select a file + to load yields a FileNotFound exception.
The workaround is to first + clear the 'Untitled' filename before selecting the file you wish + to load. +
OSX: Links don't open when clicked on or via the Sequence + or Alignment window popup menu.
OSX (Webstart): JalviewÂ only displays old news feed items